[2026-06-08T09:00:20] Launching Arriba 2.4.0
[2026-06-08T09:00:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:00:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:00:33] Reading chimeric alignments from 'aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10708629)
[2026-06-08T09:07:52] Marking multi-mapping alignments (marked=6866409)
[2026-06-08T09:07:57] Detecting strandedness (reverse)
[2026-06-08T09:07:57] Assigning strands to alignments 
[2026-06-08T09:07:59] Annotating alignments 
[2026-06-08T09:08:35] Filtering duplicates (remaining=4790072)
[2026-06-08T09:08:42] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=4510860)
[2026-06-08T09:08:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4510860)
[2026-06-08T09:08:46] Filtering viral contigs with expression lower than the top 5 (remaining=4510860)
[2026-06-08T09:08:51] Filtering viral contigs with less than 5% coverage (remaining=4510860)
[2026-06-08T09:08:54] Estimating fragment length (mate gap mean=-85.1561, mate gap stddev=30.1769, read length mean=132.072)
[2026-06-08T09:08:54] Filtering read-through fragments with a distance <=10000bp (remaining=4276965)
[2026-06-08T09:08:56] Filtering inconsistently clipped mates (remaining=4198280)
[2026-06-08T09:08:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4070386)
[2026-06-08T09:09:02] Filtering fragments with small insert size (remaining=4069554)
[2026-06-08T09:09:05] Filtering alignments with long gaps (remaining=4069554)
[2026-06-08T09:09:07] Filtering fragments with both mates in the same gene (remaining=4068859)
[2026-06-08T09:09:09] Filtering fusions arising from hairpin structures (remaining=3848756)
[2026-06-08T09:09:12] Filtering reads with a mismatch p-value <=0.01 (remaining=1738730)
[2026-06-08T09:09:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=577696)
[2026-06-08T09:09:31] Finding fusions and counting supporting reads (total=470625)
[2026-06-08T09:09:48] Merging adjacent fusion breakpoints (remaining=465759)
[2026-06-08T09:09:49] Filtering multi-mapping fusions by alignment score and read support (remaining=294469)
[2026-06-08T09:10:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:10:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=291885)
[2026-06-08T09:10:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=156473)
[2026-06-08T09:10:31] Filtering fusions with <2 supporting reads (remaining=22506)
[2026-06-08T09:10:32] Filtering fusions with an e-value >=0.3 (remaining=9166)
[2026-06-08T09:10:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9207)
[2026-06-08T09:10:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9130)
[2026-06-08T09:10:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9130)
[2026-06-08T09:10:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4463)
[2026-06-08T09:10:42] Searching for fusions with spliced split reads (remaining=4524)
[2026-06-08T09:10:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=2976)
[2026-06-08T09:10:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2943)
[2026-06-08T09:10:48] Searching for fusions with >=4 spliced events (remaining=3260)
[2026-06-08T09:10:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1015)
[2026-06-08T09:11:05] Filtering fusions with anchors <=23nt (remaining=722)
[2026-06-08T09:11:05] Filtering end-to-end fusions with low support (remaining=699)
[2026-06-08T09:11:06] Filtering fusions with no coverage around the breakpoints (remaining=683)
[2026-06-08T09:11:06] Indexing gene sequences 
[2026-06-08T09:11:11] Filtering genes with >=30% identity (remaining=281)
[2026-06-08T09:11:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-06-08T09:11:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T09:11:16] Searching for additional isoforms (remaining=169)
[2026-06-08T09:11:17] Assigning confidence scores to events 
[2026-06-08T09:11:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:11:19] Writing fusions to file 'aih-tih-sc-4e749e-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:11:20] Writing discarded fusions to file 'aih-tih-sc-4e749e-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:11:44] Freeing resources
[2026-06-08T09:12:01] Done (elapsed time=00:11:41, CPU time=00:11:40, peak memory=15.1gb)